Protein images obtained by STM, AFM and TEM

Arakawa, Hideo; Umemura, Kazuo; Ikai, Atsushi

doi:10.1038/358171a0

Cited by 70 publications

(48 citation statements)

References 17 publications

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“…Since AFM is able to image the atomic organization of both conductive and nonconductive material, it has is seen as a promising tool for biological studies (for reviews see Lal & John, 1994). A considerable number of investigators have therefore applied AFM to the observation of organic monolayers and bilayers Weisenhorn et al, 1990;Singh & Keller, 1991), ribonucleic and deoxyribonucleic acid (Thundat et al, 1992(Thundat et al, , 1993Hansma et al, 1992Hansma et al, , 1993bYang et al, 1992), amino acid crystals and proteins (Gould et al, 1988;Drake et al, 1989;Arakawa et al, 1992). There are also several reports on AFM observation of viruses, phages and in vitro cells (Butt et al, 1990;Gould et al, 1990;Henderson et al, 1992;Ikai et al, 1993;Kasas et al, 1993;Parpura et al, 1993).…”

Section: Discussionmentioning

confidence: 99%

“…Biological membranes containing phospholipid mono-, bi-and multilayers (Zasadzinski et al, 1991), individual reconstituted proteins, e.g. fibrinogen (Wigren et al, 1991), immunoglobulins Ill et al, 1993), phosphorylase kinase complexes (Edstrom et al, 1990) and alpha-macroglobulin (Arakawa et al, 1992) as well as protein arrays in lipid membranes have also been investigated (Arnsdorf & Lal, 1992;Meyerllse et al, 1992;Schabert et al, 1995) with AFM. We performed a pilot study to test the ultramicrography technique described above to obtain high-resolution images of live whole cells of E. coli and of the macromolecules lipopolysaccharide (LPS) and DNA.…”

Section: Introductionmentioning

confidence: 99%

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X‐ray microscopy and imaging of Escherichia coli, LPS and DNA

Rajyaguru

Kado

Torres

et al. 1997

Journal of Microscopy

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SummaryUltrastructural examination by transmission and scanning electron microscopy involves a series of specialized preparation steps which may introduce artefacts in the micrographs. X-ray microscopy can take instant images of specimens but is mostly restricted to a few synchrotron X-ray sources. We have utilized a bench-top nanosecond laserplasma to produce a single-shot source of nanosecond X-rays tuned for maximum contrast with carbon-rich material. To examine the ultrastructure by absorption profiles, we utilized a laser-produced plasma generated by a single-shot laser (1 . 06 mm wavelength, 5 × 10 12 W cm ¹2 intensity) focused on to a silicon target as an X-ray source for high-resolution X-ray microscopy. This approach eliminates the specimen preparation steps. Whole hydrated cells of Escherichia coli and purified preparations of lipopolysaccharide (LPS) and chromosomal DNA (cDNA) were streaked onto poly(methyl methacrylate) (PMMA)-coated grids (resist). This resist was exposed to X-rays under vacuum at a distance of 2 . 5 cm from the target disc. The silicon plasma produced by a 10-ns burst of laser energy (at 20 J) radiates strong emission lines in the region of 300 eV. The X-rays penetrate the sample and their absorption profile is transferred on to the resist where PMMA acts as a negative to generate an image. By atomic force microscopy imaging of this photoresist we have visualized layers around cells of E. coli, darker areas inside the cell probably corresponding to cDNA, and preliminary images of LPS and DNA molecules. This technique has resolution at the 100 Å level, produces images similar to the space-filling models of macromolecules and may be of great value in the study of the ultrastructure of hydrated live biological specimens.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

X‐ray microscopy and imaging of Escherichia coli, LPS and DNA

Rajyaguru

Kado

Torres

et al. 1997

Journal of Microscopy

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“…These include the fast replication of specific DNA chains (10)(11)(12), the stretching and fixation of such chains on suitably prepared substrates (13), and STM imaging. In particular, the ability to track by STM certain long polymer molecules and to identify their termination has been demonstrated (14).…”

Section: Methodological Considerationsmentioning

confidence: 99%

A scheme for sequencing large DNA molecules by identifying local nuclear-induced effects.

Kelson

Nussinov²

1994

Proc. Natl. Acad. Sci. U.S.A.

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An experimental scheme for sequencing large DNA molecules is proposed where DNA strands are replicated, with all nucleotides of a given kind marked with radioactive 32p, The marked strands are affixed to an appropriate substrate and are kept until most 32p atoms decay. The local damage caused by the decay is expected to allow the identification of the sites occupied by that particular nudeotide, using atomic scal microscopy (scanning tunnel or atomic force microscopy). Quantitative aspects and methodological considerations associated with the proposed scheme are dscs. In this paper we propose an improved method of sequencing by atomic scale scanning, which utilizes much of the existing technical capabilities. The essential feature of this proposal is the way it makes use ofradioactive nuclear decay.Marking with radioactive isotopes (e.g., with 32p) is widely used to follow specimens and substances under study or to monitor them quantitatively. However, the nuclear decay itself can induce microscopic, local physical changes in the system in which it is embedded (7). It is on such effects that our proposition is based. The Basic IdeaThe basic idea implements a conceptually simple experimental scenario. The single-stranded DNA segment that is to be sequenced is replicated in such a way that all the nucleotides of one particular type (e.g., adenine nucleotides) are incorporated into the chain with radioactive 32p. The marked molecules are then stretched and fixed onto a suitable substrate and are kept until most of the 32P nuclei decay. The effect of this decay is twofold. First, the phosphorus atom transmutes into an atom of sulfur, which does not fit chemically into the original phosphorus site and bond configuration. Second, after the decay the nucleus (and the corresponding atom) recoils with up to 78 eV of kinetic energy (8), which is sufficient to physically remove it completely from its original site. Since the phosphates form the covalent links between consecutive nucleotides, this will cut the chain at this location (9)-namely, at the site of the 32P-labeled adenine. We expect this induced break, as well as other local structural modifications, to be detectable by appropriately tuned STM (or AFM) scanning. By scanning along the chain, one can determine the length (or, equivalently, the number of nucleotides) separating consecutive adenine locations.This entire procedure is repeated for chains with completely labeled cytosine, guanine, or thymine nucleotides in turn. The four sets of scans are then combined to yield the full DNA sequence. Methodological ConsiderationsIn evaluating the feasibility and the potential advantages of the proposed method, a number of methodological observations and considerations are appropriate.(i) A number of auxiliary techniques that are essential for the implementation ofthe method are either already available or are the subject of intense development in conjunction with other methods. These include the fast replication of specific DNA chains (10)(11)(12), the stretchin...

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“…In this context transmission electron-and atomic force microscopy (TEM and AFM) are frequently used in parallel for the visual characterization of biological molecules (Arakawa et al, 1992;Lin & Goh, 2002). It has been reported that the DNA complexation with chitosans might result in a blend of structures: toroids, rods, and globules, with the relative amounts of the different structures apparently depending on the actual chitosan, the charge ratio, and solution properties like pH and ionic strength (Danielsen et al, 2004;Maurstad et al 2007).…”

Section: Structural Organizationmentioning

confidence: 99%